Organisms face continual fluctuations in global climatic processes to which they must adapt or perish. Considering that many species are key habitat formers and energy producers, such responses to climate change can have significant population, community and even ecosystem consequences. Paleo-records of ecosystem responses to past environmental variability have proven invaluable for studying impacts of climate change on natural systems, yet such records are almost completely lacking for temperate benthic marine systems. Here, we bring together recent advances in paleoclimatology, coastal geomorphology, paleoceanography and archaeology for a well-studied region (the Southern California Bight, USA). We argue that there is now enough evidence to show that late-Quaternary sea-level rise over the past 18 500 years has caused a large-scale ecological shift in this region from highly productive rocky reefs to less productive sandy shores. Our integrated approach has implications for other temperate coastlines and helps provide insight into the interactions between human culture, biological communities and their environments.